Bug 753188

Summary: Review Request: R-rtracklayer - R interface to genome browsers and their annotation tracks
Product: [Fedora] Fedora Reporter: Tom "spot" Callaway <tcallawa>
Component: Package ReviewAssignee: Pierre-YvesChibon <pingou>
Status: CLOSED ERRATA QA Contact: Fedora Extras Quality Assurance <extras-qa>
Severity: medium Docs Contact:
Priority: medium    
Version: rawhideCC: notting, package-review, pingou
Target Milestone: ---Flags: pingou: fedora-review+
gwync: fedora-cvs+
Target Release: ---   
Hardware: All   
OS: Linux   
Whiteboard:
Fixed In Version: R-GenomicFeatures-1.6.1-1.fc16 Doc Type: Bug Fix
Doc Text:
Story Points: ---
Clone Of: Environment:
Last Closed: 2011-11-29 00:04:35 UTC Type: ---
Regression: --- Mount Type: ---
Documentation: --- CRM:
Verified Versions: Category: ---
oVirt Team: --- RHEL 7.3 requirements from Atomic Host:
Cloudforms Team: --- Target Upstream Version:
Embargoed:

Description Tom "spot" Callaway 2011-11-11 14:52:32 UTC 
Spec URL: http://spot.fedorapeople.org/R-rtracklayer.spec
SRPM URL: http://spot.fedorapeople.org/R-rtracklayer-1.14.1-1.fc16.src.rpm
Description: 
Extensible framework for interacting with multiple genome browsers (currently 
UCSC built-in) and manipulating annotation tracks in various formats 
(currently GFF, BED, bedGraph, BED15, WIG, and BigWig built-in). The user may
export/import tracks to/from the supported browsers, as well as query and 
modify the browser state, such as the current viewport.
Comment 1 Pierre-YvesChibon 2011-11-11 18:47:19 UTC 
The sig.h, portimpl.h, hmmstats.h and cheapcgi.h contain the header:
/*****************************************************************************
 * Copyright (C) 2000 Jim Kent.  This source code may be freely used         *
 * for personal, academic, and non-profit purposes.  Commercial use          *
 * permitted only by explicit agreement with Jim Kent (jim_kent) *
 *****************************************************************************/

I will proceed with the review and we'll see if we can figure this licensing issue.



Package Review
==============

Key:
- = N/A
x = Check
! = Problem
? = Not evaluated



==== C/C++ ====
[x]: MUST Package does not contain any libtool archives (.la)
[x]: MUST Package does not contains kernel modules.
[x]: MUST Package contains no static executables.
[x]: MUST Rpath absent or only used for internal libs.
[x]: MUST Package is not relocatable.


==== Generic ====
[x]: MUST Package is licensed with an open-source compatible license and meets other legal requirements as defined in the legal section of Packaging Guidelines.
[x]: MUST Package successfully compiles and builds into binary rpms on at least one supported architecture.
[x]: MUST All build dependencies are listed in BuildRequires, except for any that are listed in the exceptions section of Packaging Guidelines.
[x]: MUST Package contains no bundled libraries.
[x]: MUST Changelog in prescribed format.
[x]: MUST Sources contain only permissible code or content.
[x]: MUST Macros in Summary, %description expandable at SRPM build time.
[x]: MUST Package requires other packages for directories it uses.
[x]: MUST Package uses nothing in %doc for runtime.
[x]: MUST Package is not known to require ExcludeArch.
[x]: MUST Permissions on files are set properly.
[x]: MUST Package does not contain duplicates in %files.
[x]: MUST Spec file lacks Packager, Vendor, PreReq tags.
[-]: MUST If (and only if) the source package includes the text of the license(s) in its own file, then that file, containing the text of the license(s) for the package is included in %doc.
[x]: MUST License field in the package spec file matches the actual license.
[x]: MUST Package consistently uses macros (instead of hard-coded directory names).
[x]: MUST Package meets the Packaging Guidelines.
[x]: MUST Package is named according to the Package Naming Guidelines.
[x]: MUST Package does not generates any conflict.
[x]: MUST Package obeys FHS, except libexecdir and /usr/target.
[x]: MUST Package must own all directories that it creates.
[x]: MUST Package does not own files or directories owned by other packages.
[x]: MUST Package installs properly.
[x]: MUST Requires correct, justified where necessary.
[x]: MUST Rpmlint output is silent.
[x]: MUST Sources used to build the package matches the upstream source, as provided in the spec URL.
          MD5SUM this package     : 130af70245801e131b0ebbda8fd83fde
          MD5SUM upstream package : 130af70245801e131b0ebbda8fd83fde
        
[x]: MUST Spec file is legible and written in American English.
[x]: MUST Spec file name must match the spec package %{name}, in the format %{name}.spec.
[x]: MUST Package contains a SysV-style init script if in need of one.
[x]: MUST File names are valid UTF-8.
[x]: SHOULD Reviewer should test that the package builds in mock.
[-]: SHOULD If the source package does not include license text(s) as a separate file from upstream, the packager SHOULD query upstream to include it.
[x]: SHOULD Dist tag is present.
[x]: SHOULD No file requires outside of /etc, /bin, /sbin, /usr/bin, /usr/sbin.
[x]: SHOULD Final provides and requires are sane (rpm -q --provides and rpm -q --requires).
[x]: SHOULD Package functions as described.
[-]: SHOULD Package does not include license text files separate from upstream.
[x]: SHOULD SourceX is a working URL.
[-]: SHOULD Description and summary sections in the package spec file contains translations for supported Non-English languages, if available.
[-]: SHOULD Package should compile and build into binary rpms on all supported architectures.
   Checked on x86_64
[-]: SHOULD %check is present and all tests pass.
[x]: SHOULD Packages should try to preserve timestamps of original installed files.
[x]: SHOULD Spec use %global instead of %define.


==== R ====
[x]: MUST Package contains the mandatory BuildRequires.
[x]: MUST The package has the standard %build section.
[x]: MUST The package owns the created directory.
[x]: MUST Package have the default element marked as %doc : 
[x]: MUST Package requires R-core.
[x]: SHOULD The %check macro is present
[x]: SHOULD Latest version is packaged.

Let's see for the licensing issue then.
Comment 2 Tom "spot" Callaway 2011-11-14 14:34:09 UTC 
Jim Kent, the upstream copyright holder for those files, has given permission via email to use/modify/distribute them under the terms of the BSD license.

New SPEC: http://spot.fedorapeople.org/R-rtracklayer.spec
New SRPM: http://spot.fedorapeople.org/R-rtracklayer-1.14.1-2.fc16.src.rpm
Comment 3 Pierre-YvesChibon 2011-11-14 14:43:21 UTC 
Ok this package is then approved.
Comment 4 Tom "spot" Callaway 2011-11-14 15:27:31 UTC 
New Package SCM Request
=======================
Package Name: R-rtracklayer
Short Description: R interface to genome browsers and their annotation tracks
Owners: spot
Branches: f15 f16
InitialCC:
Comment 5 Gwyn Ciesla 2011-11-14 15:54:42 UTC 
Git done (by process-git-requests).
Comment 6 Fedora Update System 2011-11-15 16:12:28 UTC 
R-GenomicFeatures-1.6.1-1.fc15,R-biomaRt-2.10.0-1.fc15,R-rtracklayer-1.14.1-2.fc15,R-RCurl-1.7.0-2.fc15,R-Rcompression-0.93.2-3.fc15,R-affydata-1.11.15-2.fc15,R-BSgenome.Celegans.UCSC.ce2-1.3.17-2.fc15,R-hgu95av2probe-2.9.0-1.fc15,R-hgu95av2cdf-2.9.1-1.fc15,R-hgu133acdf-2.9.1-1.fc15,R-BSgenome-1.22.0-1.fc15,R-ROC-1.30.0-1.fc15,R-multtest-2.10.0-2.fc15,R-maanova-1.24.0-1.fc15,R-fibroEset-1.4.6-1.fc15,R-Biostrings-2.22.0-1.fc15,R-bigmemory-4.2.11-1.fc15,R-AnnotationDbi-1.16.0-2.fc15,R-affy-1.32.0-1.fc15,R-RM2-0.0-8.fc15,R-GenomicRanges-1.6.2-1.fc15,R-biglm-0.8-1.fc15,R-Biobase-2.14.0-2.fc15,R-XML-3.4.3-2.fc15,R-timeDate-2131.00-1.fc15,R-caTools-1.12-2.fc15,R-BufferedMatrixMethods-1.18.0-1.fc15,R-IRanges-1.12.1-1.fc15,R-tkWidgets-1.32.0-2.fc15,R-RSQLite-0.10.0-1.fc15,R-msm-1.1-1.fc15,R-lmtest-0.9.29-1.fc15,R-xtable-1.6.0-1.fc15,R-wavethresh-4.5-2.fc15,R-waveslim-1.6.4-2.fc15,R-statmod-1.4.13-1.fc15,R-sciplot-1.0.9-1.fc15,R-Rsolid-0.9.31-5.fc15,R-RScaLAPACK-0.6.1-8.fc15,scalapack-1.7.5-14.fc15,R-rlecuyer-0.3.1-3.fc15,R-qvalue-1.28.0-1.fc15,R-hdf5-1.6.9-13.fc15,R-GeneR-2.24.0-2.fc15,R-combinat-0.0.8-1.fc15,R-BufferedMatrix-1.18.0-2.fc15,R-bitops-1.0.4.1-6.fc15,R-widgetTools-1.32.0-2.fc15,R-DynDoc-1.32.0-2.fc15,R-preprocessCore-1.16.0-2.fc15,R-RUnit-0.4.26-3.fc15,R-affyio-1.22.0-1.fc15,R-acepack-1.3.3.0-1.fc15,R-abind-1.3.0-1.fc15,R-RODBC-1.3.3-1.fc15,R-qtl-1.21.2-2.fc15,R-nws-1.7.0.1-3.fc15,R-mvtnorm-0.9.9991-1.fc15,R-zoo-1.7.6-2.fc15,R-DBI-0.2.5-3.fc15,rpy-2.2.4-1.fc15,rkward-0.5.7-2.fc15.1,graphviz-2.26.3-6.fc15,R-2.14.0-3.fc15 has been submitted as an update for Fedora 15.
https://admin.fedoraproject.org/updates/R-GenomicFeatures-1.6.1-1.fc15,R-biomaRt-2.10.0-1.fc15,R-rtracklayer-1.14.1-2.fc15,R-RCurl-1.7.0-2.fc15,R-Rcompression-0.93.2-3.fc15,R-affydata-1.11.15-2.fc15,R-BSgenome.Celegans.UCSC.ce2-1.3.17-2.fc15,R-hgu95av2probe-2.9.0-1.fc15,R-hgu95av2cdf-2.9.1-1.fc15,R-hgu133acdf-2.9.1-1.fc15,R-BSgenome-1.22.0-1.fc15,R-ROC-1.30.0-1.fc15,R-multtest-2.10.0-2.fc15,R-maanova-1.24.0-1.fc15,R-fibroEset-1.4.6-1.fc15,R-Biostrings-2.22.0-1.fc15,R-bigmemory-4.2.11-1.fc15,R-AnnotationDbi-1.16.0-2.fc15,R-affy-1.32.0-1.fc15,R-RM2-0.0-8.fc15,R-GenomicRanges-1.6.2-1.fc15,R-biglm-0.8-1.fc15,R-Biobase-2.14.0-2.fc15,R-XML-3.4.3-2.fc15,R-timeDate-2131.00-1.fc15,R-caTools-1.12-2.fc15,R-BufferedMatrixMethods-1.18.0-1.fc15,R-IRanges-1.12.1-1.fc15,R-tkWidgets-1.32.0-2.fc15,R-RSQLite-0.10.0-1.fc15,R-msm-1.1-1.fc15,R-lmtest-0.9.29-1.fc15,R-xtable-1.6.0-1.fc15,R-wavethresh-4.5-2.fc15,R-waveslim-1.6.4-2.fc15,R-statmod-1.4.13-1.fc15,R-sciplot-1.0.9-1.fc15,R-Rsolid-0.9.31-5.fc15,R-RScaLAPACK-0.6.1-8.fc15,scalapack-1.7.5-14.fc15,R-rlecuyer-0.3.1-3.fc15,R-qvalue-1.28.0-1.fc15,R-hdf5-1.6.9-13.fc15,R-GeneR-2.24.0-2.fc15,R-combinat-0.0.8-1.fc15,R-BufferedMatrix-1.18.0-2.fc15,R-bitops-1.0.4.1-6.fc15,R-widgetTools-1.32.0-2.fc15,R-DynDoc-1.32.0-2.fc15,R-preprocessCore-1.16.0-2.fc15,R-RUnit-0.4.26-3.fc15,R-affyio-1.22.0-1.fc15,R-acepack-1.3.3.0-1.fc15,R-abind-1.3.0-1.fc15,R-RODBC-1.3.3-1.fc15,R-qtl-1.21.2-2.fc15,R-nws-1.7.0.1-3.fc15,R-mvtnorm-0.9.9991-1.fc15,R-zoo-1.7.6-2.fc15,R-DBI-0.2.5-3.fc15,rpy-2.2.4-1.fc15,rkward-0.5.7-2.fc15.1,graphviz-2.26.3-6.fc15,R-2.14.0-3.fc15
Comment 7 Fedora Update System 2011-11-15 16:13:38 UTC 
R-GenomicFeatures-1.6.1-1.fc16,R-biomaRt-2.10.0-1.fc16,R-rtracklayer-1.14.1-2.fc16,R-RCurl-1.7.0-2.fc16,R-Rcompression-0.93.2-3.fc16,R-affydata-1.11.15-2.fc16,R-BSgenome.Celegans.UCSC.ce2-1.3.17-2.fc16,R-hgu95av2probe-2.9.0-1.fc16,R-hgu95av2cdf-2.9.1-1.fc16,R-hgu133acdf-2.9.1-1.fc16,R-BSgenome-1.22.0-1.fc16,R-ROC-1.30.0-1.fc16,R-multtest-2.10.0-2.fc16,R-maanova-1.24.0-1.fc16,R-fibroEset-1.4.6-1.fc16,R-Biostrings-2.22.0-1.fc16,R-bigmemory-4.2.11-1.fc16,R-AnnotationDbi-1.16.0-2.fc16,R-affy-1.32.0-1.fc16,R-RM2-0.0-8.fc16,R-GenomicRanges-1.6.2-1.fc16,R-biglm-0.8-1.fc16,R-Biobase-2.14.0-2.fc16,R-XML-3.4.3-2.fc16,R-timeDate-2131.00-1.fc16,R-caTools-1.12-2.fc16,R-BufferedMatrixMethods-1.18.0-1.fc16,R-IRanges-1.12.1-1.fc16,R-tkWidgets-1.32.0-2.fc16,R-RSQLite-0.10.0-1.fc16,R-msm-1.1-1.fc16,R-lmtest-0.9.29-1.fc16,R-xtable-1.6.0-1.fc16,R-wavethresh-4.5-2.fc16,R-waveslim-1.6.4-2.fc16,R-statmod-1.4.13-1.fc16,R-sciplot-1.0.9-1.fc16,R-Rsolid-0.9.31-5.fc16,R-RScaLAPACK-0.6.1-8.fc16,scalapack-1.7.5-14.fc16,R-rlecuyer-0.3.1-3.fc16,R-qvalue-1.28.0-1.fc16,R-hdf5-1.6.9-13.fc16,R-GeneR-2.24.0-2.fc16,R-combinat-0.0.8-1.fc16,R-BufferedMatrix-1.18.0-2.fc16,R-bitops-1.0.4.1-6.fc16,R-widgetTools-1.32.0-2.fc16,R-DynDoc-1.32.0-2.fc16,R-preprocessCore-1.16.0-2.fc16,R-RUnit-0.4.26-3.fc16,R-affyio-1.22.0-1.fc16,R-acepack-1.3.3.0-1.fc16,R-abind-1.3.0-1.fc16,R-RODBC-1.3.3-1.fc16,R-qtl-1.21.2-2.fc16,R-nws-1.7.0.1-3.fc16,R-mvtnorm-0.9.9991-1.fc16,R-zoo-1.7.6-2.fc16,R-DBI-0.2.5-3.fc16,rpy-2.2.4-1.fc16,rkward-0.5.7-2.fc16,graphviz-2.28.0-10.fc16,R-2.14.0-3.fc16 has been submitted as an update for Fedora 16.
https://admin.fedoraproject.org/updates/R-GenomicFeatures-1.6.1-1.fc16,R-biomaRt-2.10.0-1.fc16,R-rtracklayer-1.14.1-2.fc16,R-RCurl-1.7.0-2.fc16,R-Rcompression-0.93.2-3.fc16,R-affydata-1.11.15-2.fc16,R-BSgenome.Celegans.UCSC.ce2-1.3.17-2.fc16,R-hgu95av2probe-2.9.0-1.fc16,R-hgu95av2cdf-2.9.1-1.fc16,R-hgu133acdf-2.9.1-1.fc16,R-BSgenome-1.22.0-1.fc16,R-ROC-1.30.0-1.fc16,R-multtest-2.10.0-2.fc16,R-maanova-1.24.0-1.fc16,R-fibroEset-1.4.6-1.fc16,R-Biostrings-2.22.0-1.fc16,R-bigmemory-4.2.11-1.fc16,R-AnnotationDbi-1.16.0-2.fc16,R-affy-1.32.0-1.fc16,R-RM2-0.0-8.fc16,R-GenomicRanges-1.6.2-1.fc16,R-biglm-0.8-1.fc16,R-Biobase-2.14.0-2.fc16,R-XML-3.4.3-2.fc16,R-timeDate-2131.00-1.fc16,R-caTools-1.12-2.fc16,R-BufferedMatrixMethods-1.18.0-1.fc16,R-IRanges-1.12.1-1.fc16,R-tkWidgets-1.32.0-2.fc16,R-RSQLite-0.10.0-1.fc16,R-msm-1.1-1.fc16,R-lmtest-0.9.29-1.fc16,R-xtable-1.6.0-1.fc16,R-wavethresh-4.5-2.fc16,R-waveslim-1.6.4-2.fc16,R-statmod-1.4.13-1.fc16,R-sciplot-1.0.9-1.fc16,R-Rsolid-0.9.31-5.fc16,R-RScaLAPACK-0.6.1-8.fc16,scalapack-1.7.5-14.fc16,R-rlecuyer-0.3.1-3.fc16,R-qvalue-1.28.0-1.fc16,R-hdf5-1.6.9-13.fc16,R-GeneR-2.24.0-2.fc16,R-combinat-0.0.8-1.fc16,R-BufferedMatrix-1.18.0-2.fc16,R-bitops-1.0.4.1-6.fc16,R-widgetTools-1.32.0-2.fc16,R-DynDoc-1.32.0-2.fc16,R-preprocessCore-1.16.0-2.fc16,R-RUnit-0.4.26-3.fc16,R-affyio-1.22.0-1.fc16,R-acepack-1.3.3.0-1.fc16,R-abind-1.3.0-1.fc16,R-RODBC-1.3.3-1.fc16,R-qtl-1.21.2-2.fc16,R-nws-1.7.0.1-3.fc16,R-mvtnorm-0.9.9991-1.fc16,R-zoo-1.7.6-2.fc16,R-DBI-0.2.5-3.fc16,rpy-2.2.4-1.fc16,rkward-0.5.7-2.fc16,graphviz-2.28.0-10.fc16,R-2.14.0-3.fc16
Comment 8 Fedora Update System 2011-11-16 00:24:45 UTC 
Package R-GenomicFeatures-1.6.1-1.fc16, R-biomaRt-2.10.0-1.fc16, R-rtracklayer-1.14.1-2.fc16, R-RCurl-1.7.0-2.fc16, R-Rcompression-0.93.2-3.fc16, R-affydata-1.11.15-2.fc16, R-BSgenome.Celegans.UCSC.ce2-1.3.17-2.fc16, R-hgu95av2probe-2.9.0-1.fc16, R-hgu95av2cdf-2.9.1-1.fc16, R-hgu133acdf-2.9.1-1.fc16, R-BSgenome-1.22.0-1.fc16, R-ROC-1.30.0-1.fc16, R-multtest-2.10.0-2.fc16, R-maanova-1.24.0-1.fc16, R-fibroEset-1.4.6-1.fc16, R-Biostrings-2.22.0-1.fc16, R-bigmemory-4.2.11-1.fc16, R-AnnotationDbi-1.16.0-2.fc16, R-affy-1.32.0-1.fc16, R-RM2-0.0-8.fc16, R-GenomicRanges-1.6.2-1.fc16, R-biglm-0.8-1.fc16, R-Biobase-2.14.0-2.fc16, R-XML-3.4.3-2.fc16, R-timeDate-2131.00-1.fc16, R-caTools-1.12-2.fc16, R-BufferedMatrixMethods-1.18.0-1.fc16, R-IRanges-1.12.1-1.fc16, R-tkWidgets-1.32.0-2.fc16, R-RSQLite-0.10.0-1.fc16, R-msm-1.1-1.fc16, R-lmtest-0.9.29-1.fc16, R-xtable-1.6.0-1.fc16, R-wavethresh-4.5-2.fc16, R-waveslim-1.6.4-2.fc16, R-statmod-1.4.13-1.fc16, R-sciplot-1.0.9-1.fc16, R-Rsolid-0.9.31-5.fc16, R-RScaLAPACK-0.6.1-8.fc16, scalapack-1.7.5-14.fc16, R-rlecuyer-0.3.1-3.fc16, R-qvalue-1.28.0-1.fc16, R-hdf5-1.6.9-13.fc16, R-GeneR-2.24.0-2.fc16, R-combinat-0.0.8-1.fc16, R-BufferedMatrix-1.18.0-2.fc16, R-bitops-1.0.4.1-6.fc16, R-widgetTools-1.32.0-2.fc16, R-DynDoc-1.32.0-2.fc16, R-preprocessCore-1.16.0-2.fc16, R-RUnit-0.4.26-3.fc16, R-affyio-1.22.0-1.fc16, R-acepack-1.3.3.0-1.fc16, R-abind-1.3.0-1.fc16, R-RODBC-1.3.3-1.fc16, R-qtl-1.21.2-2.fc16, R-nws-1.7.0.1-3.fc16, R-mvtnorm-0.9.9991-1.fc16, R-zoo-1.7.6-2.fc16, R-DBI-0.2.5-3.fc16, rpy-2.2.4-1.fc16, rkward-0.5.7-2.fc16, graphviz-2.28.0-10.fc16, R-2.14.0-3.fc16:
* should fix your issue,
* was pushed to the Fedora 16 testing repository,
* should be available at your local mirror within two days.
Update it with:
# su -c 'yum update --enablerepo=updates-testing R-GenomicFeatures-1.6.1-1.fc16 R-biomaRt-2.10.0-1.fc16 R-rtracklayer-1.14.1-2.fc16 R-RCurl-1.7.0-2.fc16 R-Rcompression-0.93.2-3.fc16 R-affydata-1.11.15-2.fc16 R-BSgenome.Celegans.UCSC.ce2-1.3.17-2.fc16 R-hgu95av2probe-2.9.0-1.fc16 R-hgu95av2cdf-2.9.1-1.fc16 R-hgu133acdf-2.9.1-1.fc16 R-BSgenome-1.22.0-1.fc16 R-ROC-1.30.0-1.fc16 R-multtest-2.10.0-2.fc16 R-maanova-1.24.0-1.fc16 R-fibroEset-1.4.6-1.fc16 R-Biostrings-2.22.0-1.fc16 R-bigmemory-4.2.11-1.fc16 R-AnnotationDbi-1.16.0-2.fc16 R-affy-1.32.0-1.fc16 R-RM2-0.0-8.fc16 R-GenomicRanges-1.6.2-1.fc16 R-biglm-0.8-1.fc16 R-Biobase-2.14.0-2.fc16 R-XML-3.4.3-2.fc16 R-timeDate-2131.00-1.fc16 R-caTools-1.12-2.fc16 R-BufferedMatrixMethods-1.18.0-1.fc16 R-IRanges-1.12.1-1.fc16 R-tkWidgets-1.32.0-2.fc16 R-RSQLite-0.10.0-1.fc16 R-msm-1.1-1.fc16 R-lmtest-0.9.29-1.fc16 R-xtable-1.6.0-1.fc16 R-wavethresh-4.5-2.fc16 R-waveslim-1.6.4-2.fc16 R-statmod-1.4.13-1.fc16 R-sciplot-1.0.9-1.fc16 R-Rsolid-0.9.31-5.fc16 R-RScaLAPACK-0.6.1-8.fc16 scalapack-1.7.5-14.fc16 R-rlecuyer-0.3.1-3.fc16 R-qvalue-1.28.0-1.fc16 R-hdf5-1.6.9-13.fc16 R-GeneR-2.24.0-2.fc16 R-combinat-0.0.8-1.fc16 R-BufferedMatrix-1.18.0-2.fc16 R-bitops-1.0.4.1-6.fc16 R-widgetTools-1.32.0-2.fc16 R-DynDoc-1.32.0-2.fc16 R-preprocessCore-1.16.0-2.fc16 R-RUnit-0.4.26-3.fc16 R-affyio-1.22.0-1.fc16 R-acepack-1.3.3.0-1.fc16 R-abind-1.3.0-1.fc16 R-RODBC-1.3.3-1.fc16 R-qtl-1.21.2-2.fc16 R-nws-1.7.0.1-3.fc16 R-mvtnorm-0.9.9991-1.fc16 R-zoo-1.7.6-2.fc16 R-DBI-0.2.5-3.fc16 rpy-2.2.4-1.fc16 rkward-0.5.7-2.fc16 graphviz-2.28.0-10.fc16 R-2.14.0-3.fc16'
as soon as you are able to.
Please go to the following url:
https://admin.fedoraproject.org/updates/FEDORA-2011-15910
then log in and leave karma (feedback).
Comment 9 Fedora Update System 2011-11-29 00:04:35 UTC 
R-GenomicFeatures-1.6.1-1.fc15, R-biomaRt-2.10.0-1.fc15, R-rtracklayer-1.14.1-2.fc15, R-RCurl-1.7.0-2.fc15, R-Rcompression-0.93.2-3.fc15, R-affydata-1.11.15-2.fc15, R-BSgenome.Celegans.UCSC.ce2-1.3.17-2.fc15, R-hgu95av2probe-2.9.0-1.fc15, R-hgu95av2cdf-2.9.1-1.fc15, R-hgu133acdf-2.9.1-1.fc15, R-BSgenome-1.22.0-1.fc15, R-ROC-1.30.0-1.fc15, R-multtest-2.10.0-2.fc15, R-maanova-1.24.0-1.fc15, R-fibroEset-1.4.6-1.fc15, R-Biostrings-2.22.0-1.fc15, R-bigmemory-4.2.11-1.fc15, R-AnnotationDbi-1.16.0-2.fc15, R-affy-1.32.0-1.fc15, R-RM2-0.0-8.fc15, R-GenomicRanges-1.6.2-1.fc15, R-biglm-0.8-1.fc15, R-Biobase-2.14.0-2.fc15, R-XML-3.4.3-2.fc15, R-timeDate-2131.00-1.fc15, R-caTools-1.12-2.fc15, R-BufferedMatrixMethods-1.18.0-1.fc15, R-IRanges-1.12.1-1.fc15, R-tkWidgets-1.32.0-2.fc15, R-RSQLite-0.10.0-1.fc15, R-msm-1.1-1.fc15, R-lmtest-0.9.29-1.fc15, R-xtable-1.6.0-1.fc15, R-wavethresh-4.5-2.fc15, R-waveslim-1.6.4-2.fc15, R-statmod-1.4.13-1.fc15, R-sciplot-1.0.9-1.fc15, R-Rsolid-0.9.31-5.fc15, R-RScaLAPACK-0.6.1-8.fc15, scalapack-1.7.5-14.fc15, R-rlecuyer-0.3.1-3.fc15, R-qvalue-1.28.0-1.fc15, R-hdf5-1.6.9-13.fc15, R-GeneR-2.24.0-2.fc15, R-combinat-0.0.8-1.fc15, R-BufferedMatrix-1.18.0-2.fc15, R-bitops-1.0.4.1-6.fc15, R-widgetTools-1.32.0-2.fc15, R-DynDoc-1.32.0-2.fc15, R-preprocessCore-1.16.0-2.fc15, R-RUnit-0.4.26-3.fc15, R-affyio-1.22.0-1.fc15, R-acepack-1.3.3.0-1.fc15, R-abind-1.3.0-1.fc15, R-RODBC-1.3.3-1.fc15, R-qtl-1.21.2-2.fc15, R-nws-1.7.0.1-3.fc15, R-mvtnorm-0.9.9991-1.fc15, R-zoo-1.7.6-2.fc15, R-DBI-0.2.5-3.fc15, rpy-2.2.4-1.fc15, rkward-0.5.7-2.fc15.1, graphviz-2.26.3-6.fc15, R-2.14.0-3.fc15 has been pushed to the Fedora 15 stable repository.  If problems still persist, please make note of it in this bug report.
Comment 10 Fedora Update System 2011-11-29 00:13:35 UTC 
R-GenomicFeatures-1.6.1-1.fc16, R-biomaRt-2.10.0-1.fc16, R-rtracklayer-1.14.1-2.fc16, R-RCurl-1.7.0-2.fc16, R-Rcompression-0.93.2-3.fc16, R-affydata-1.11.15-2.fc16, R-BSgenome.Celegans.UCSC.ce2-1.3.17-2.fc16, R-hgu95av2probe-2.9.0-1.fc16, R-hgu95av2cdf-2.9.1-1.fc16, R-hgu133acdf-2.9.1-1.fc16, R-BSgenome-1.22.0-1.fc16, R-ROC-1.30.0-1.fc16, R-multtest-2.10.0-2.fc16, R-maanova-1.24.0-1.fc16, R-fibroEset-1.4.6-1.fc16, R-Biostrings-2.22.0-1.fc16, R-bigmemory-4.2.11-1.fc16, R-AnnotationDbi-1.16.0-2.fc16, R-affy-1.32.0-1.fc16, R-RM2-0.0-8.fc16, R-GenomicRanges-1.6.2-1.fc16, R-biglm-0.8-1.fc16, R-Biobase-2.14.0-2.fc16, R-XML-3.4.3-2.fc16, R-timeDate-2131.00-1.fc16, R-caTools-1.12-2.fc16, R-BufferedMatrixMethods-1.18.0-1.fc16, R-IRanges-1.12.1-1.fc16, R-tkWidgets-1.32.0-2.fc16, R-RSQLite-0.10.0-1.fc16, R-msm-1.1-1.fc16, R-lmtest-0.9.29-1.fc16, R-xtable-1.6.0-1.fc16, R-wavethresh-4.5-2.fc16, R-waveslim-1.6.4-2.fc16, R-statmod-1.4.13-1.fc16, R-sciplot-1.0.9-1.fc16, R-Rsolid-0.9.31-5.fc16, R-RScaLAPACK-0.6.1-8.fc16, scalapack-1.7.5-14.fc16, R-rlecuyer-0.3.1-3.fc16, R-qvalue-1.28.0-1.fc16, R-hdf5-1.6.9-13.fc16, R-GeneR-2.24.0-2.fc16, R-combinat-0.0.8-1.fc16, R-BufferedMatrix-1.18.0-2.fc16, R-bitops-1.0.4.1-6.fc16, R-widgetTools-1.32.0-2.fc16, R-DynDoc-1.32.0-2.fc16, R-preprocessCore-1.16.0-2.fc16, R-RUnit-0.4.26-3.fc16, R-affyio-1.22.0-1.fc16, R-acepack-1.3.3.0-1.fc16, R-abind-1.3.0-1.fc16, R-RODBC-1.3.3-1.fc16, R-qtl-1.21.2-2.fc16, R-nws-1.7.0.1-3.fc16, R-mvtnorm-0.9.9991-1.fc16, R-zoo-1.7.6-2.fc16, R-DBI-0.2.5-3.fc16, rpy-2.2.4-1.fc16, rkward-0.5.7-2.fc16, graphviz-2.28.0-10.fc16, R-2.14.0-3.fc16 has been pushed to the Fedora 16 stable repository.  If problems still persist, please make note of it in this bug report.